The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize

Abstract

BackgroundAs metabolic pathway resources become more commonly available, researchers have unprecedented access to information about their organism of interest. Despite efforts to ensure consistency between various resources, information content and quality can vary widely. Two maize metabolic pathway resources for the B73 inbred line, CornCyc 4.0 and MaizeCyc 2.2, are based on the same gene model set and were developed using Pathway Tools software. These resources differ in their initial enzymatic function assignments and in the extent of manual curation. We present an in-depth comparison between CornCyc and MaizeCyc to demonstrate the effect of initial computational enzymatic function assignments on the quality and content of metabolic pathway resources.ResultsThese two resources are different in their content. MaizeCyc contains GO annotations for over 21,000 genes that CornCyc is missing. CornCyc contains on average 1.6 transcripts per gene, while MaizeCyc contains almost no alternate splicing. MaizeCyc also does not match CornCyc’s breadth in representing the metabolic domain; MaizeCyc has fewer compounds, reactions, and pathways than CornCyc. CornCyc’s computational predictions are more accurate than those in MaizeCyc when compared to experimentally determined function assignments, demonstrating the relative strength of the enzymatic function assignment pipeline used to generate CornCyc.ConclusionsOur results show that the quality of initial enzymatic function assignments primarily determines the quality of the final metabolic pathway resource. Therefore, biologists should pay close attention to the methods and information sources used to develop a metabolic pathway resource to gauge the utility of using such functional assignments to construct hypotheses for experimental studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-016-0369-x) contains supplementary material, which is available to authorized users.

Opaque-2 Regulates a Complex Gene Network Associated with Cell Differentiation and Storage Functions of Maize Endosperm

“…The most significant biological process enriched for this target gene set is "carboxylic acid metabolic process," which is associated with 16 genes, including the LKR/SDH, cyPPDK1, and cyPPDK2 genes, while the other two enriched biological processes are "glutamine family amino acid biosynthetic process" and "proline catabolic process." Consistent with the GO term enrichments, an analysis of metabolic pathways associated with the O2-activated direct targets using the CornCyc tool (Walsh et al, 2016) revealed genes involved in glycine biosynthesis, l-glutamine biosynthesis, proline metabolism (as part of the l-N δ -acetylornithine biosynthesis pathway), and l-glutamate degradation (Supplemental Data Set 4). Together, these GO term enrichments and pathway associations indicate that O2 directly activates genes encoding storage proteins and enzymes involved in amino acid synthesis and metabolism.…”

An adaptive teosintemexicanaintrogression modulates phosphatidylcholine levels and is associated with maize flowering time

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MaizeGDB 2018: the maize multi-genome genetics and genomics database

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